twenty-six February: "--recode vcf" heading changed getting being compatible with VCFtoolspact a thousand Genomes phase 1 analysis data released into the information web page.
Single-reliability digital matrix yields (elizabeth
2 February: --bcf today handles BCFv2.2 nonzero lost genotype and you will end-of-vector philosophy (released because of the age.g. bcftools step 
one.1) securely. --mendel-multigen no longer is blocked of the demand-line parser whenever a family-situated connection shot try focus on. --shed, --freq, --robust, and you may --het now help gzipped production (add the 'gz' modifier). --Roentgen put in creativity create.
fifteen January: --keep/--beat now work properly towards the recently-current IDs when --update-ids is within the exact same focus on. --mac/--max-mac computer set in development make.
several January: --dosage + --covar + --gender today really works safely, and you may a wrong caution towards PLINK step 1.07 implementation might have been eliminated. --serving logistic regression not accounts incorrect p-viewpoints having very small products.
(beta 3): --epistasis implemented, with heavy optimization for quantitative traits. "--recode vcf<,-fid,-iid>" now flags reference alleles as "possibly not based on a real reference genome" unless --real-ref-alleles is also specified, and sets ALT alleles to '.' when they are not present in the immediate dataset. --vcf-min-gq and --vcf-min-gp no longer error out when a genotype entry has fewer fields than expected, since the VCF specification explicitly states that this is an acceptable way to represent trailing missing values. --make-bed no longer segfaults when resorting a file too large to fit in memory.
: --dummy, --show-tags, --neighbor, --mh/--bd/--mh2/--homog and you will --clump-profession bugfixes. --q-score-range observed for dosage data. --split-x/--merge-x 'no-fail' modifier added to service investigation sales programs.
Digital --range efficiency bugfix
thirteen December: Case/manage --hardy/--hwe don't randomly excludes so many controls away from manage-simply phase from test. (This was generally simple, while the all of the-trials take to nonetheless spent some time working, while the insect was only attending exist whenever --hardy/--hwe was in a similar work with because the other filters including --exclude/--pull. But when you used the UNAFF rows throughout the --robust report getting things, you should rerun --sturdy for the current build. ) set-test multiple-review modification now matters nonempty establishes with no significant versions.
7 December: --to switch now applies to the new mutual try figure instead of the ingredient perception in the event the previous try calculated, without longer profile linearly genomic-controlled p-thinking after they might possibly be invalid. Particular numeric balances developments getting quick p-opinions. --logistic permutation ensure that you --assoc/--design place-try bugfixes. --linear/--logistic place-make sure --dosage 'sex' modifier then followed. --serving + --intercourse error message today explains you to PLINK step one.07 don't deal with that it flag combination securely.
twenty-five November: Fixed --exclude/--extract thoughts administration bug in 2 November make. --get now supporting amount study. --write-amount no more writes incorrect IDs whenever decide to try filters was used. --serving 'noheader' may now be studied with 'list' when for each batch only has one file. --assoc/--design lay-try then followed. --set-missing-var-ids prolonged permitting addition out-of allele brands, and you will --set-missing-snp-ids/--set-missing-nonsnp-ids resigned. UNADJ column beliefs are now correct within the "--to alter gc" account.
2 November: Improved version ID browse speed. grams. --make-grm-bin) is becoming predicated on twice-precision internal data, and also the 'bin' + 'single-prec' modifier combination could have been replaced with 'bin4'.
15 October: Fixed an insect when you look at the --vcf's management of versions having 10 or maybe more alternative alleles. --dosage Zout don't segfaults towards the bottom. Merger no longer scrambles centimorgan coordinates.
20 Sep: Fixed low-rigid --biallelic-simply insect whenever addressing multiallelic variations. When you have utilized --biallelic-only without 'strict' into VCF records which have triallelic variations, we highly recommend rerunning the latest operation to your current generate. Repaired decimal trait --assoc bug you to definitely brought about they to type for every output line double, and you may --linear/--logistic mishandling of a few datasets with heterozygous haploid calls. --vcf-min-gp put into innovation make.
18 Sep: --no-fid bugfix. Presence off nonnumeric phenotype chain (e.grams. 'NA') no more push this new phenotype is handled once the decimal. --output-missing-phenotype today welcomes nonnumeric chain. "--dose list" today really works securely with multiple batches. --oxford-single-chr banner added to ensure it is packing regarding single-chromosome .gen files having ignorable SNP ID occupation viewpoints. --genome no further fails to statement particular mother-young children relationships. --update-alleles was still shed several fits involving missing genotypes; it has been fixed.
